\documentclass[chap]{mst_thesis}
\usepackage{epsfig}
\usepackage{graphicx}
\usepackage{algorithmic}
\usepackage{algorithm}
\usepackage[fleqn]{amsmath}
\usepackage{amssymb}
\usepackage{url}
\usepackage{comment}
\usepackage{amsthm}
\usepackage{subfigure}

% added by Ben
\usepackage{makeidx}
\makeindex
%\usepackage{nomencl}
%\usepackage[dvips]{graphicx,color}
%\usepackage{amsmath} % advanced math
%\usepackage{verbatim} % multi-line comments
%\usepackage{appendix}
% see http://www.tug.org/applications/hyperref/manual.html
\usepackage[breaklinks=true, % allow links to break over lines by making links over multiple lines into PDF links to the same target 
hyperindex, % Makes the page numbers of index entries into hyperlinks. 
%backref, 
pagebackref, % Adds backlink text to the end of each item in the bibliography, as a list of page numbers. 
linktocpage, % make page number, not text, be link on TOC, LOF and LOT 
colorlinks=false, 
pdftitle={Dissertation introduction}, 
pdfauthor={Ben Payne}, 
pdfsubject={comprehensive exam}, 
pdfkeywords={exam comprehensive dissertation introduction anderson localization random media gain}]{hyperref}
\usepackage{glossary}
\makeglossary  % http://texblog.wordpress.com/2007/11/01/glossary-in-latex/

%\usepackage[left=1.5in,top=1in,right=1.25in,bottom=.3in]{geometry} %For the stupid, stupid margins
\newcommand {\remline} {\vspace{-12pt}}

% Use the first command below if you want captions over 1 line indented. A side
% effect of this is to remove the use of bold for captions. To restore bold,
% also include the second line below.
%\usepackage[hang]{caption}  
% change the caption delimiter in caption2.sty from a colon to a period:
%\renewcommand\captionlabeldelim{.}

\usepackage{hangcaption}

% The following command will specify the correct graphics driver for the
% graphics routines used with LaTeX.  Possible options include:
% template, dvips, oztex, textures, dvialw, emtex, dvilaser, psprint,
% dvipsone, dvi2ps, pctexps, pctex32, pctexwin, pctexhp, pubps,
% dviwin, dvitops, ln, dvipsnames.
\ExecuteOptions{textures}

%\includeonly{MSTchap1}  % use \includeonly to process only
                         % the file(s) listed inside the braces
                         % separate more than one file with a comma
\begin{document}
% Leave the following lines alone:
\addtocontents{toc}{\hfill Page}%for "Page" at top of TOC 
\addtocontents{lof}{\noindent Figure \hfill Page}%for the Figures page
\addtocontents{loa}{\noindent Algorithm \hfill Page}
\addtocontents{lot}{\noindent Table \hfill Page}%for the Tables page
\addtocontents{los}{\noindent \protect\makebox[1in][l]{\underline{Symbol}} \underline{Description} \hfill \\}%for the Symbols page 

\include{chapters/title}      % title page material

\include{chapters/abstract}   % abstract page
\include{chapters/acknowledgements}        % acknowledgements page
\tableofcontents     % table of contents (automatically generated)
\listoffigures       % required if there are figures (automatically generated)
%\listofalgorithms
\listoftables        % required if there are tables (automatically generated)
\nomenclature        % required if there are variables (automatically generated
                     % if you use the \symbol command)
%\include{chapters/appendix_symbols_used}

% Leave the following line alone:
\addtocontents{toc}{\parindent0pt\vskip12pt SECTION} %toc entry

% note: each included file should start with \section{X}
\include{chapters/introduction_draft2}
% history
% current passive criteria
% mention self-embedding
\include{chapters/oned}
% model comparsion, tunneling
% T/E
\include{chapters/quasi1d}
% closed channels
% regimes plot
% criteria
\include{chapters/quasi3d}
\include{chapters/conclusion}

% Leave the following two lines alone:
\appendix            % This command is used only once!
                     % It resets the formatting for the appendices.
\include{chapters/appendix_layman_overview}
\include{chapters/appendix_1d_transfer_matrix_and_AB_derivation}
\include{chapters/appendix_1d_energy_in_one_slab_derivation}
\include{chapters/appendix_alpha_beta_convention}
\include{chapters/appendix_q1d_single_scatterer_derivation}
\include{chapters/appendix_q1d_double_scatterer_derivation}
\include{chapters/appendix_open_closed_channel_folding}
\include{chapters/appendix_self-embedding_derivation}
\include{chapters/appendix_transmission_derivation}

\specialhead{BIBLIOGRAPHY}
\remline
%\singlespace
\bibliography{../../research/latex_bibliography}
%%%\bibliographystyle{abbrv}  % numbered alphabetical list
\bibliographystyle{unsrt} % in order to citation

\addcontentsline{toc}{chapter}{Curriculum Vitae}
\include{chapters/vita}

\newpage 
\printglossary
% make sure the glossary shows up in table of contents:
\addcontentsline{toc}{chapter}{Glossary}

\newpage
\printindex
\addcontentsline{toc}{chapter}{Index}

\end{document}